Contacts of the strand formed by residues 1225 - 1234 (chain I) in PDB entry 6ASX


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with VAL1225 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    803I  ALA*     5.2     1.3    -      -       +      -
    804I  PHE      4.2     4.7    -      -       -      +
    805I  MET*     4.5    15.7    -      -       +      -
   1209I  GLN*     3.2     4.9    -      -       -      -
   1210I  ILE*     2.9    34.4    +      -       -      +
   1212I  LEU*     3.7    41.1    -      -       +      +
   1221I  PHE*     5.3     7.6    -      -       +      -
   1222I  GLU      5.0     0.9    -      -       -      +
   1223I  ARG      3.6     6.7    -      -       -      +
   1224I  PRO*     1.3    75.0    -      -       +      +
   1226I  THR*     1.3    68.2    +      -       -      +
   1227I  VAL      3.7     0.5    +      -       -      -
    636J  GLY*     3.5    34.1    -      -       -      +
    638J  SER*     3.7    12.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR1226 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    803I  ALA*     3.1     5.9    -      -       -      +
    804I  PHE*     3.0    46.5    +      -       +      -
   1112I  ILE*     5.3     1.6    -      -       +      -
   1115I  THR*     4.0    10.8    -      -       +      -
   1116I  HIS*     3.9    20.5    +      -       +      +
   1208I  GLY      4.4     2.0    -      -       -      +
   1209I  GLN*     3.8    16.9    +      -       -      +
   1225I  VAL*     1.3    73.8    -      -       -      +
   1227I  VAL*     1.3    69.2    +      -       -      +
    638J  SER*     3.0    13.9    +      -       -      -
    639J  VAL      2.9    24.9    +      -       -      +
    640J  GLY*     4.1     1.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1227 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    801I  ARG*     4.1    20.6    -      -       -      +
    802I  VAL      3.1     8.5    -      -       -      +
    803I  ALA*     3.7    16.4    -      -       +      -
   1088I  ASP*     6.4     0.2    -      -       +      -
   1094I  VAL*     4.6     9.4    -      -       +      -
   1115I  THR*     3.9    10.2    -      -       -      +
   1116I  HIS*     4.9     1.2    -      -       -      -
   1119I  MET*     4.3    12.8    -      -       +      +
   1208I  GLY      4.0    11.3    +      -       -      +
   1210I  ILE*     3.7    33.2    -      -       +      -
   1212I  LEU*     3.7    30.3    -      -       +      -
   1225I  VAL*     3.7     3.3    +      -       +      +
   1226I  THR*     1.3    83.0    -      -       -      +
   1228I  GLY*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY1228 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    801I  ARG*     3.1     9.9    -      -       -      +
    802I  VAL*     2.8    28.8    +      -       -      -
   1115I  THR*     3.6    18.3    -      -       -      +
   1119I  MET*     3.7    16.4    -      -       -      -
   1227I  VAL*     1.3    79.6    -      -       -      +
   1229I  TYR*     1.3    66.9    +      -       -      -
   1230I  MET      4.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR1229 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    699I  LEU*     4.1    15.1    -      -       +      +
    700I  VAL*     5.3     1.9    -      -       -      +
    799I  ASN*     4.5     9.1    -      -       +      +
    800I  MET*     3.4     8.3    -      -       -      +
    801I  ARG*     3.4    62.9    +      -       +      +
   1114I  GLU*     4.0    10.0    -      -       -      +
   1115I  THR*     3.7    10.2    +      -       -      +
   1118I  GLY*     3.9    26.0    -      -       -      +
   1119I  MET*     4.0    12.0    -      -       +      +
   1122I  LYS*     3.5    53.9    -      -       +      +
   1126I  ASP*     5.4     1.2    +      -       -      -
   1228I  GLY*     1.3    76.3    -      -       -      -
   1230I  MET*     1.3    61.6    +      -       -      +
   1231I  TYR      4.2     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET1230 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    799I  ASN*     4.2     1.8    -      -       -      -
    800I  MET*     2.9    30.5    +      -       -      +
    802I  VAL*     3.8    19.1    -      -       +      +
    804I  PHE*     3.7    22.9    -      -       +      -
   1068I  GLY*     5.2     5.2    -      -       -      -
   1069I  ARG      6.1     0.7    -      -       -      +
   1070I  HIS*     6.3     0.2    -      -       -      -
   1072I  ASN*     4.0    19.7    -      -       -      +
   1098I  LEU*     4.6     7.6    -      -       +      -
   1111I  GLN*     3.9    24.5    -      -       +      +
   1114I  GLU*     4.5    17.0    -      -       +      +
   1115I  THR*     3.4    23.6    -      -       -      +
   1229I  TYR*     1.3    74.7    -      -       -      +
   1231I  TYR*     1.3    65.3    +      -       -      +
   1232I  MET*     3.4    28.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR1231 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    686I  GLN*     5.9     0.2    -      -       -      -
    696I  ASP      3.9     9.4    -      -       -      -
    697I  LYS      4.0     0.7    -      -       -      -
    698I  PRO*     3.7    32.3    -      -       +      -
    699I  LEU      5.3     2.2    -      -       -      +
    700I  VAL      5.9     0.7    -      -       -      +
    795I  ALA*     3.2     5.4    -      -       -      -
    796I  LEU*     2.6    25.6    +      -       +      -
    797I  GLY*     2.5    52.6    +      -       -      -
    798I  GLN*     3.6    15.7    -      -       -      -
    799I  ASN*     3.7    12.8    -      -       +      +
   1068I  GLY*     4.3     7.4    -      -       -      -
   1069I  ARG*     3.8    34.3    +      -       -      +
   1114I  GLU*     4.0    15.7    +      -       -      +
   1229I  TYR      4.2     0.6    +      -       -      -
   1230I  MET*     1.3    76.1    -      -       -      +
   1232I  MET*     1.3    59.4    +      -       -      +
   1233I  LEU*     3.8    15.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET1232 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    797I  GLY*     3.4     1.6    -      -       -      -
    798I  GLN      2.9    34.8    +      -       -      +
    800I  MET*     3.7    13.9    -      -       +      +
    802I  VAL*     5.0     4.9    -      -       -      -
    816I  ILE*     3.7    31.2    -      -       +      -
    828I  PHE*     4.3     7.1    -      -       +      -
   1066I  MET*     4.2    13.2    -      -       +      -
   1067I  ALA*     3.4    20.9    -      -       -      +
   1068I  GLY*     4.8     0.9    -      -       -      +
   1072I  ASN*     5.7     2.5    -      -       -      +
   1096I  ILE*     3.7    35.0    -      -       +      -
   1098I  LEU*     4.7     9.6    -      -       +      -
   1230I  MET*     3.4    26.8    +      -       +      +
   1231I  TYR*     1.3    76.0    -      -       -      +
   1233I  LEU*     1.3    62.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1233 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    685I  MET      3.9    21.3    -      -       -      +
    686I  GLN*     4.0    14.1    -      -       +      -
    689I  ALA*     3.9    22.2    -      -       +      -
    796I  LEU*     4.1     9.9    -      -       +      -
    797I  GLY*     4.2    16.8    -      -       -      +
    828I  PHE*     4.5     4.9    -      -       -      -
   1066I  MET*     3.3     6.6    -      -       -      +
   1067I  ALA*     2.9    33.8    +      -       +      +
   1068I  GLY      4.2    11.0    -      -       -      +
   1069I  ARG*     3.9    21.1    -      -       +      -
   1231I  TYR*     3.8    21.5    -      -       +      +
   1232I  MET*     1.3    79.8    -      -       -      +
   1234I  LYS*     1.3    61.1    +      -       -      +
   1235I  LEU*     4.6     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1234 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    689I  ALA*     3.7     2.3    -      -       -      +
    690I  VAL*     3.3    43.2    +      -       +      +
    692I  THR*     5.5     4.6    -      -       +      +
    797I  GLY*     5.3     1.8    -      -       -      -
    828I  PHE*     3.4    44.3    +      -       +      +
    830I  THR*     3.6    15.4    -      -       +      +
   1058I  ARG      4.0     1.0    +      -       -      -
   1059I  ARG      2.9    28.5    +      -       -      -
   1060I  ILE*     4.7     4.4    -      -       +      +
   1064I  ASP*     4.4    16.8    +      -       +      -
   1065I  LYS      4.1     6.3    -      -       -      +
   1066I  MET*     4.3     8.1    -      -       +      -
   1233I  LEU*     1.3    73.4    -      -       -      +
   1235I  LEU*     1.3    69.4    +      -       -      +
   1238I  LEU*     4.0    30.8    -      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il